BrisBio Network Series: Session #2
Researcher Speaker: Dr Jake Bradford
Abstract
High performance bioinformatics software for CRISPR technologies
CRISPR has become a leading tool for gene editing, due to the ability to make targeted modifications in virtually any genome of interest. The technology relies on using a customisable βguide RNAβ sequence that controls where the modifications will be made. Designing high quality guide RNAs is not trivial and is a computationally expensive task. In this presentation, I will discuss software solutions for solving the complex biological questions associated with CRISPR technologies.
HDR Speaker: Oliver Hughes
Abstract
Robust and reproducible results are essential for confident scientific analysis. We demonstrate that transcription factor (TF) Chromatin Immunoprecipitation coupled with sequencing (ChIP-seq) suffers from systematic bias that may threaten its reproducibility: 80% of 200+ condition-matched, dual-replicate experiments in ENCODE contain genomic regions of systematic bias. We observe this regional bias even between replicates produced within the same experiment, resulting in thousands of irreproducible peaks, which contain valuable biological data. We provide evidence that regional bias may lead to qualitative differences in TF biology inferred by different experiments; we discovered eight TFs with binding activity in compact chromatin that was identified by one experiment, yet systematically absent from others. To mitigate the effects of bias, we derive simple but effective metrics to quantify the quality of data within biased regions and demonstrate that they can be used for the robust integration of data from multiple replicates or experiments.
